# HG changeset patch
# User chrisw
# Date 1549996957 18000
# Node ID 1f0e3aaaba194990acfb39aec1b2d74092aefd18
Uploaded
diff -r 000000000000 -r 1f0e3aaaba19 .shed.yml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/.shed.yml Tue Feb 12 13:42:37 2019 -0500
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+categories:
+- Statistics
+description: bamcount is a tools for efficiently summarizing coverage information from a BAM file
+long_description: |
+ bamcount is a tool for efficiently computing coverage statistics over a DNA/RNA BAM file.
+ It is aligner agnostic and counts everything over only one pass through the BAM.
+ https://github.com/BenLangmead/bamcount
+name: bamcount
+owner: ChristoperWilks
+remote_repository_url: https://github.com/ChristopherWilks/bamcount_galaxy
+type: unrestricted
diff -r 000000000000 -r 1f0e3aaaba19 bamcount.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bamcount.xml Tue Feb 12 13:42:37 2019 -0500
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+
+
+ bamcount
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+ [options]
+
+ Options:
+ -h --help Show this screen.
+ --version Show version.
+ --threads # of threads to do BAM decompression
+
+ Non-reference summaries:
+ --alts Print differing from ref per-base coverages
+ Writes to a CSV file .alts.tsv
+ --include-softclip Print a record for soft-clipped bases
+ --include-n Print mismatch records when mismatched read base is N
+ --print-qual Print quality values for mismatched bases
+ --delta Print POS field as +/- delta from previous
+ --require-mdz Quit with error unless MD:Z field exists everywhere it's
+ expected
+ --no-head Don't print sequence names and lengths in header
+
+ Coverage and quantification:
+ --coverage Print per-base coverage (slow but totally worth it)
+ --auc Print per-base area-under-coverage, will generate it for the genome
+ and for the annotation if --annotation is also passed in
+ Writes to a TSV file .auc.tsv
+ --bigwig Output coverage as BigWig file(s). Writes to .all.bw
+ (also .unique.bw when --min-unique-qual is specified).
+ Requires libBigWig.
+ --annotation
+ Path to BED file containing list of regions to sum coverage over
+ (tab-delimited: chrm,start,end)
+ --min-unique-qual
+ Output second bigWig consisting built only from alignments
+ with at least this mapping quality. --bigwig must be specified.
+ Also produces second set of annotation sums based on this coverage
+ if --annotation is enabled
+ --double-count Allow overlapping ends of PE read to count twice toward
+ coverage
+ --num-bases Report total sum of bases in alignments processed (that pass filters)
+
+ Other outputs:
+ --read-ends Print counts of read starts/ends, if --min-unique-qual is set
+ then only the alignments that pass that filter will be counted here
+ Writes to 2 TSV files: .starts.tsv, .ends.tsv
+ --frag-dist Print fragment length distribution across the genome
+ Writes to a TSV file .frags.tsv
+ --echo-sam Print a SAM record for each aligned read
+ --ends Report end coordinate for each read (useful for debugging)
+ ]]>
+
+
+@misc{githubbamcount,
+ author = {Wilks, Christopher},
+ year = {2019},
+ title = {bamcount},
+ publisher = {GitHub},
+ journal = {GitHub repository},
+ url = {https://github.com/BenLangmead/bamcount},
+}
+
+
diff -r 000000000000 -r 1f0e3aaaba19 test-data/test.bam
Binary file test-data/test.bam has changed
diff -r 000000000000 -r 1f0e3aaaba19 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Tue Feb 12 13:42:37 2019 -0500
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